rs10510905

chr3-63811196-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_171774.1(CDHR18P):n.110+2332A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0833 in 152,250 control chromosomes in the GnomAD database, including 1,226 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.083 (1226 hom., cov: 32)
• Consequence: CDHR18P NR_171774.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.23

Genes affected

CDHR18P (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDHR18P	NR_171774.1	n.110+2332A>G		intron_variant, non_coding_transcript_variant
C3orf49	XM_047447470.1	c.-79-12054T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000443346.1	n.622+15628A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0830 AC: 12633 AN: 152132 Hom.: 1221 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.0528

Gnomad ASJ AF: 0.0325

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.0329

Gnomad FIN AF: 0.0200

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0218

Gnomad OTH AF: 0.0828

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0833 AC: 12677 AN: 152250 Hom.: 1226 Cov.: 32 AF XY: 0.0802 AC XY: 5971 AN XY: 74438

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.0527

Gnomad4 ASJ AF: 0.0325

Gnomad4 EAS AF: 0.00309

Gnomad4 SAS AF: 0.0331

Gnomad4 FIN AF: 0.0200

Gnomad4 NFE AF: 0.0218

Gnomad4 OTH AF: 0.0829

Alfa AF: 0.0587 Hom.: 85

Bravo AF: 0.0907

Asia WGS AF: 0.0400 AC: 140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.13
Dann	Benign	0.41

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10510905; hg19: chr3-63796872;